biogems.info - gems for bioinformatics

New: CloudBioLinux packages are now listed on biogems.info !

#	biogem	description	by	version	released	stars	issues	total	90d*)	7d	90d**)
								downloads		commits
1	bio	Bioinformatics library (...)	BioRuby project	1.4.3.0001	20 months	30	12	83909	8534
2	biodiversity	Parser of scientific names (...)	Dmitry Mozzherin	3.1.5	5 months	18	5	43673	3929
3	simple spreadsheet extractor	Basic spreadsheet content extraction using apache poi (...)	Stuart Owen, Finn Bacall, Quyen Nguyen	0.13.4	2 weeks	5	1	38653	4415
4	bio gem	Biogem is a software generator for Ruby in (...)	Raoul J.P. Bonnal, Pjotr Prins	1.3.6	8 months	14	11	35020	2845
5	bio samtools	Binder of samtools for Ruby, on the top (...)	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal	2.2.0	3 months	17	5	31652	4470	0	0
6	t2 server	Support for interacting with taverna 2 server (...)	Robert Haines, Finn Bacall	1.2.0	4 months	2	...	27291	3275	0	9
7	bio ucsc api	The Ruby ucsc api: accessing the ucsc genome (...)	Hiroyuki Mishima, Jan Aerts	0.6.2	10 months	13	1	22628	2155	0	0
8	entrez	Http requests to entrez e-utilities (...)	Jared Ning	0.5.8.1	3 years	4	...	21804	1641
9	biomart	A Ruby api for interacting with biomart services (...)	Darren Oakley	0.2.3	3 years	17	4	21621	1266
10	bio gadget	Gadgets for bioinformatics (...)	Shintaro Katayama	0.4.8	20 months		...	21457	2723
11	taverna t2flow	Support for interacting with taverna 2 workflows (...)	Finn Bacall, Robert Haines, David Withers et al.	0.5.1	10 months		...	21054	2935
12	sequenceserver	Blast search made easy! (...)	Anurag Priyam, Ben J Woodcroft, Yannick Wurm	0.8.9	7 weeks	30	19	18787	1923	34	126
13	bio gff3	Gff3 parser for big data (...)	Pjotr Prins	0.9.1	2 years	6	2	17339	1254	0	0
14	bio svgenes	Create pretty svg-format images of features, gene models (...)	Dan MacLean	0.4.1	13 months	9	5	16214	3331	0	0
15	bio maf	Maf parser for BioRuby (...)	Clayton Wheeler	1.0.1	2 years	10	30	16170	1658
16	search biomodel	Interfaces with biomodel search engine (...)	Niall Beard	2.1.6	2 years		...	14779	1148	0	0
17	bio grid	A biogem to submit jobs on a queue (...)	Francesco Strozzi	0.3.3	2 years	5	...	13979	1486	0	0
18	bio logger	Log4r wrapper with extra features for roles and (...)	Pjotr Prins	1.0.1	2 years	4	2	13872	1672	0	0
19	obo parser	A simple obo file handler (...)	mjy	0.3.7	3 years	4	...	12946	859
20	bio blastxmlparser	Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...)	Pjotr Prins	2.0.2	2 months	12	...	12936	2409
21	bio faster	A fast parser for fastq files (...)	Francesco Strozzi	0.4.5	2 years	9	...	10210	877	0	0
22	bio alignment	Support for multiple sequence alignments (msa) (...)	Pjotr Prins	0.0.8	8 months	7	5	9944	913
23	bio table	Swiss army knife of tabulated data; transforming/filtering tab/csv (...)	Pjotr Prins	1.0.0	8 months	8	20	9715	1148	0	0
24	biointerchange	An open source framework for transforming heterogeneous data (...)	Joachim Baran, Kevin B. Cohen, Geraint Duck et al.	1.0.8	3 weeks	10	2	8808	2067	0	23
25	bio phyta	Pipeline to remove contaminations from est libraries (...)	Philipp Comans	0.9.4	3 years	1	1	8642	615	0	0
26	bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha (...)	George Githinji	0.7.1	23 months	1	...	8630	765	0	0
27	nexus parser	A nexus file format (phylogenetic inference) parser in (...)	mjy	1.1.4	3 years	1	...	8324	487
28	bio bigbio	Low memory sequence emitters (...)	Pjotr Prins	0.1.6	8 months	8	1	8184	748	0	0
29	bio band	Data mining algorithms for jRuby (...)	arrigonialberto86	0.1.11	16 months	14	3	8181	1384	0	0
30	scaffolder	Build genome output files (...)	Michael Barton	0.5.0	17 months	5	...	7884	529	0	0
31	taverna baclava	Ruby support for the baclava file format (...)	Robert Haines	1.0.1	11 months	1	...	7822	1850	0	0
32	bio signalp	A wrapper for the signal peptide prediction algorith (...)	Ben J Woodcroft	0.3.1	6 months	1	...	7611	756	0	0
33	bio assembly	BioRuby assembly plugin (...)	Chase Miller, Francesco Strozzi	0.1.0	4 years	4	...	7589	497
34	rubyMorphbank	Simple morphbank (http://morphbank.net) services accessor (...)	mjy	0.2.6	3 years	1	...	7503	477	0	0
35	bio tm hmm	A BioRuby plugin for interaction with the transmembrane (...)	Ben J. Woodcroft	0.2.2	2 years	2	...	7211	622	0	0
36	bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org) (...)	Rutger Vos, Anurag Priyam	1.1.0	2 years	7	2	7078	503	0	0
37	eutils	Lightweight Ruby api for ncbi eutils (...)	Joon Lee, aka seouri	0.2.1	19 months	8	...	7038	520	0	0
38	bioportal	Supports linking of models within a ror application (...)	Stuart Owen, Quyen Nguyen	2.2	10 months		...	6932	2170	0	0
39	bio isoelectric point	A BioRuby plugin for calculating the isoelectric point (...)	George Githinji, Pascal Betz	0.1.3	2 years	3	...	6893	519
40	bio sambamba	Ruby wrapper for sambamba tool (...)	Artem Tarasov	0.0.5	2 years	2	...	6890	636	0	0
41	bio kmer counter	A biogem for counting small kmers for fingerprinting (...)	Ben J Woodcroft	0.1.2	20 months	5	...	6863	748	0	0
42	genfrag	This is a development release (...)	Pjotr Prins and Trevor Wennblom	0.0.0.4	5 years			6818	421
43	bio graphics	Library for visualizing genomic regions (...)	Jan Aerts	1.4	7 years	22	1	6490	390	0	0
44	bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps (...)	Hiroyuki Mishima	0.1.2	3 years	4	...	6311	406	0	0
45	bio ngs	Bio-ngs provides a framework for handling ngs data (...)	Francesco Strozzi, Raoul J.P. Bonnal	0.5.2	2 years	29	14	6066	392	0	0
46	bio octopus	Running and parsing of the protein transmembrane domain (...)	Ben J Woodcroft	0.1.1	3 years	1	...	5792	379	0	0
47	bio bgzf	Reading/writing bgzf blocks (...)	Artem Tarasov, Clayton Wheeler	0.2.1	2 years	2	...	5243	538	0	0
48	bio bwa	Ruby binding for bwa mapping software (...)	Francesco Strozzi	0.2.2	3 years	4	...	5101	388	0	0
49	goruby	Gene ontology (go) interface for Ruby (...)	Ben J Woodcroft	0.2.0	4 years	9	...	5000	281	0	0
50	bio lazyblastxml	A plugin that allows you to parse large (...)	robsyme	0.4.0	3 years	1	...	4889	381	0	0
51	bio polyploid tools	Tool to work with polyploids, ngs and molecular (...)	Ricardo H. Ramirez-Gonzalez	0.5.2	3 months	2	...	4780	2062
52	bio basespace sdk	Basespace Ruby sdk is a Ruby based software (...)	Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.	0.1.7	18 months	11	2	4715	902	0	0
53	bio pileup iterator	Iterate through a samtools pileup file (...)	Ben J. Woodcroft	0.0.4	2 years	2	...	4686	368	0	0
54	ruby ensembl api	Api to ensembl databases (...)	Jan Aerts, Francesco Strozzi	1.0.1	4 years	30	5	4680	238	0	0
55	bio cd hit report	Read and manipulate cd-hit clusters (...)	George Githinji	0.1.0	21 months	2	1	4565	497	0	0
56	bio tabix	Ruby binding for samtools tabix (...)	throwern	1.0.1	16 months	3	...	4303	513
57	taverna player	Taverna player is a rails plugin to run (...)	Robert Haines	0.10.0	3 months	4	3	3911	871	0	4
58	bio kb illumina	Geneexpression illuminahumanannotation (...)	Raoul J.P. Bonnal	0.1.0	4 years	1	...	3874	251	0	0
59	bio gff3 pltools	Ruby wrapper for the gff3-pltools (...)	Marjan Povolni	0.3.0	2 years			3874	379
60	bio plasmoap	Implementation of the plasmoap algorithm (...)	Ben J Woodcroft	0.0.2	3 years	1	...	3836	248	0	0
61	bio chembl	Chembl rest api client, parser and container (...)	Mitsuteru Nakao	0.1.3	2 years	1	1	3819	393	0	0
62	bio gngm	Next-generation mapping of mutations (...)	Dan MacLean	0.2.1	2 years	2	...	3797	385	0	0
63	bio ucsc util	Ruby binding to the ucsc kent utilities (...)	throwern	0.1.2	2 years	2	...	3786	363
64	bio rdf	Bioinformatics triple-store support (...)	Pjotr Prins	0.0.2	2 years	4	1	3601	280	0	3
65	bio affy	Parse affymetrix cel/cdf files (...)	Pjotr Prins	0.5.1	3 years	2	1	3555	279	0	0
66	bio core	BioRuby core plugins, most and stable plugins. blastxmlparser, (...)	Raoul J.P. Bonnal	0.0.1	3 years	1	...	3322	255	0	0
67	bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal (...)	Ben J. Woodcroft	0.3.0	2 years	1	...	3151	259	0	0
68	bio velvet	Parser to work with file formats used in (...)	Ben J Woodcroft	0.6.0	3 weeks		...	3114	1050	0	8
69	bio wolf psort wrapper	Enables the localisation predictor wolf psort to be (...)	Ben J Woodcroft	0.0.3	3 years	1	...	3090	252
70	bio statsample timeseries	Timeseries modules for statsample (...)	Ankur Goel, Claudio Bustos	0.2.1	16 months		...	3084	522
71	bio unichem	BioRuby plugin for unichem rest web service (...)	Mitsuteru Nakao	0.3.0	24 months		...	3012	367
72	bio vcf	Fast multi-threaded vcf parser (...)	Pjotr Prins	0.8.2	5 weeks	15	6	3001	1230
73	bio synreport	Reports whether a nucleotide change results in synonymous (...)	Dan MacLean	0.1.2	20 months		...	2895	371	0	0
74	bio krona	This biogem is built around krona, a flashy (...)	Ben J. Woodcroft	0.1.1	17 months	1	...	2890	389	0	0
75	bio hmmer model	Parse pfam hmm definition files (...)	Ben J. Woodcroft	0.0.2	2 years	1	...	2761	256	0	0
76	bio protparam	A protparam compatible utility for BioRuby (...)	hryk	0.2.0	2 years	1	...	2703	255	0	0
77	bio gag	Bio-gag is a biogem for detecting and correcting (...)	Ben J Woodcroft	0.1.0	2 years	2	...	2602	252	0	0
78	publisci	Publish scientific results to the semantic web (...)	Will Strinz	0.1.6	7 months	3	16	2292	352	0	0
79	bio polymarker db batch	Server for polymarker. to be used with cron (...)	Ricardo H. Ramirez-Gonzalez	0.4.0	3 months		...	2097	972	0	0
80	bio sge	BioRuby plugin for sun grid engine (...)	Toshiaki Katayama	0.0.0	4 years	4	...	2017	126	0	0
81	bio hello	Hello world plugin for the BioRuby (just for (...)	Toshiaki Katayama	0.0.0	4 years	3	...	1998	131	0	0
82	bio restriction enzyme	Digests dna based on restriction enzyme cut patterns (...)	Trevor Wennblom	1.0.0	3 years		1	1997	132	0	0
83	bio liftover	Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)	Andrei Rozanski	1.3.0	10 months	1	...	1931	515	0	0
84	dna sequence aligner	Does high pairwise alignment of sequencing reads with (...)	John T. Prince	0.0.2	4 years	1	...	1926	125
85	rubyBHL	Rubybhl is a simple request/response wrapper for the (...)	Matt Yoder	0.2.1	11 months	6	...	1854	173
86	bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of (...)	Ben J Woodcroft	0.1.0	3 years	1	...	1740	125	0	0
87	bio core ext	BioRuby core ext: plugins which require external library (...)	Raoul J.P. Bonnal, Pjotr Prins	0.0.1	3 years	1	...	1728	120	0	0
88	bio data restriction enzyme	Restriction enzyme dataset (...)	Sir Richard J. Roberts, Trevor Wennblom	1.109.0	3 years		...	1709	133	0	0
89	bio biolinux	Meta package for biolinux distribution (...)	Raoul J.P. Bonnal	0.1.0	3 years	2	...	1702	136	0	0
90	bio ensembl	A Ruby api to the ensembl database (...)	Jan Aerts, Francesco Strozzi	1.1.0	3 years	3	...	1678	120	0	0
91	bio foo	One-line summary of your gem (...)	Toshiaki Katayama	0.0.0	3 years	1	...	1670	131	0	0
92	bio dbsnp	Decoding the dbsnp bitfield (...)	Hiroyuki Mishima	0.1.1	3 years	4	...	1657	136
93	bio phyloxml	Phyloxml plugin for BioRuby (...)	Diana Jaunzeikare, Clayton Wheeler	0.9.0	2 years	3	...	1632	129	0	0
94	bio gggenome	Gggenome Ruby client (...)	Mitsuteru Nakao	0.2.0	17 months	1	...	1626	251	0	0
95	bio exportpred	Wrapper around the exportpred algorithm for predicting p (...)	Ben J Woodcroft	0.0.1	3 years	1	...	1612	128	0	0
96	bio aliphatic index	A simple biogem that allows computation of the (...)	Ben J Woodcroft	0.0.1	3 years	1	...	1599	129	0	0
97	bio hydropathy	Hydropathy scale for BioRuby (...)	Ben J Woodcroft	0.0.1	3 years	1	...	1583	124	0	0
98	taxonifi	A general purpose framework for scripted handling of (...) development/stable	mjy	0.2.0	22 months	1	...	1560	150
99	bio ensembl rest	Ruby ensembl rest api (...)	Alberto Donizetti	0.2.0	16 months	3	1	1541	250	0	0
100	bio hmmer3 report	Enables parsing of hmmer version 3 reports (...)	Christian Zmasek, Ben J Woodcroft	0.0.1	2 years	1	1	1488	136	0	0
101	bio statsample glm	Generalized linear models for statsample (...)	Ankur Goel	0.1.1	16 months		...	1487	248
102	bio velvet underground	Bindings to some internals of the velvet assembler (...)	Ben Woodcroft	0.3.0	3 weeks		1	1412	718	0	9
103	bio incanter	Build graph with jRuby (...)	Matteo Picciolini	0.1.0	2 years		...	1396	134
104	bio biostars analytics	Biostars data-mining and statistical analysis (...)	Joachim Baran	0.2.0	9 months	1	...	1393	386	0	0
105	bio ipcress	A programmatic interface to the ipcress in-silico pcr (...)	Ben J Woodcroft	0.0.1	2 years	1	...	1390	132	0	0
106	intermine bio	Biological extensions for the intermine webservice client library (...)	Alex Kalderimis	0.98.1	3 years		...	1388	93
107	bio commandeer	Dead simple method of running shell commands from (...)	Ben J. Woodcroft	0.1.0	12 months		...	1229	253	0	0
108	bio express beta diversity	Interface for express beta diversity (...)	Ben J. Woodcroft	0.1.0	12 months		...	1211	264	0	0
109	bio repeatmasker	Bio-repeatmasker (...)	Andrei Rozanski	0.0.3	12 months			1197	258
110	bio img metadata	Reads metadata from integrated microbial genomes (img) metadata (...)	Ben J. Woodcroft	0.0.1	2 years		...	1139	132	0	0
111	ref2bibtex	Pass a full citation, get the bibtex back, (...)	Matt Yoder	0.0.3	2 months		...	1089	709
112	bio cigar	A parser for cigar format alignments (...)	Ben J Woodcroft	0.1.0	11 months	4	...	1055	269	0	0
113	nbio cloudquery	Client for xoopit's cloudquery api (...)	Cameron Walters, nb.io	0.1.5	5 years	4	...	1028	355
114	bio stockholm	Parse stockholm sequence alignment format (...)	Ben J. Woodcroft	0.0.1	19 months	2	...	924	128	0	0
115	bio samtools server	Web server for bio-samtools (...)	homonecloco	0.1.2	8 months		...	909	269	0	0
116	bio raxml	Ruby wrapper to run standard-raxml for maximum likelihood (...)	Fernando Izquierdo	0.1.0	18 months		...	863	132	0	0
117	bio locus	Fast storage and comparison of chr+pos(+alt) locations (...)	Pjotr Prins	0.0.6	3 months		...	696	283
118	bio exominer	Mine publications for gene names (...)	Pjotr Prins	0.0.3	11 months		...	534	139	0	0
119	nbio csshttprequest	Csshttprequest is cross-domain ajax using css as a (...)	Cameron Walters, Randy Reddig	1.0.3	6 years	30	1	521	183
120	genomichdt	A restful service for sharing genomic data (...)	Joachim Baran, Robert Buels, Michel Dumontier	0.0.1	10 months	2	...	430	113	0	0
121	bio qtlHD	(...) pre		pre				385	19
122	bio kseq	Ruby inferface for kseq.h by heng li for (...)	Fedor Gusev	0.0.2	6 months		...	380	145
123	bio sra	A sequence read archive (sra) download script and (...)	Ben J. Woodcroft	0.2.0	6 weeks	1	...	357	357	0	11
124	bark	A Ruby wrapper on the open tree api (...) beta	Matt Yoder	0.0.2	4 months		...	303	154
125	bio faidx	Tools to work with fasta files, indexed with (...)	homonecloco	0.0.1	3 months		...	296	162	0	0
126	bio blat tools	Tools to manipulate blat files from the command (...)	homonecloco	0.1.0	4 months		...	283	143	0	0
127	nbio css http request	Csshttprequest is cross-domain ajax using css (...)	Cameron Walters, Randy Reddig	0.1	6 years			272	97
128	bio location rdfize	Faldo location output method for bio::location in BioRuby (...)	Joachim Baran, Naohisa Goto	0.0.0	11 weeks		...	235	235	0	16
129	bio old biofetch emulator	Emulates as if old BioRuby biofetch alives (...)	Naohisa Goto	0.0.0	11 weeks		...	234	234	0	10
130	bio primer3	(...) pre		pre				127	28
131	bio rocker	Rocker (...) new	Luis (Coto) Orellana, Luis M. Rodriguez-R	0.1.0	1 week			114	114

*) gem downloads (total & last 90 days) from rubygems.org as of 2015-02-01
**) number of commits on GitHub (last 7 days & last 90 days)